Contacts of the helix formed by residues 4986 - 4996 (chain F) in PDB entry 6X34
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR4986 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4175F ARG 3.9 20.2 + - - -
4176F ILE* 4.6 14.6 - - + -
4177F GLU 5.3 1.8 + - - -
4190F PHE* 6.1 2.5 - + - -
4200F TRP* 5.4 0.4 - - - -
4229F PHE* 4.4 23.6 - + + -
4233F CYS* 5.3 1.3 - - - -
4958F ILE* 4.5 15.4 + - + -
4959F CYS* 5.6 1.6 + - - -
4979F GLU 5.4 0.2 + - - -
4980F GLU 3.7 19.1 + - - -
4981F HIS* 4.5 2.6 - - - -
4982F ASN* 4.3 3.7 + - + -
4983F LEU* 3.7 35.7 + - - -
4984F ALA* 3.0 14.5 - - - +
4985F ASN* 1.3 75.8 - - - +
4987F MET* 1.3 64.3 + - - +
4988F PHE 3.1 1.1 - - - -
4989F PHE* 3.1 26.5 + + + +
4990F LEU* 3.4 15.0 + - + +
5020F PHE* 4.4 21.5 - + + -
5021F PRO* 5.9 5.7 - - + +
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Residues in contact with MET4987 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4196F ASN* 4.4 5.5 + - - +
4200F TRP* 4.3 23.5 - - + -
4229F PHE* 5.8 0.4 - - - -
4233F CYS* 4.3 28.2 - - + -
4236F THR* 4.4 13.0 - - + +
4237F ILE* 4.5 11.1 - - + +
4985F ASN 3.2 0.6 - - - -
4986F TYR* 1.3 79.3 - - - +
4988F PHE* 1.3 56.5 + - - +
4990F LEU* 3.4 5.9 + - - +
4991F MET* 2.9 27.0 + - - +
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Residues in contact with PHE4988 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4190F PHE* 4.5 6.2 - - + -
4192F ILE* 4.2 27.8 - - + -
4193F SER 6.0 0.2 - - - +
4196F ASN* 3.2 28.0 + - + +
4200F TRP* 6.1 0.2 - - - -
4985F ASN* 3.2 17.7 + - + +
4986F TYR 3.1 0.6 - - - -
4987F MET* 1.3 77.2 - - - +
4989F PHE* 1.3 58.4 + - - +
4991F MET* 3.3 7.1 + - - +
4992F TYR* 2.9 27.9 + - - +
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Residues in contact with PHE4989 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4176F ILE* 4.7 13.5 - - + -
4178F ILE* 5.0 12.8 - - + -
4188F ILE* 4.7 12.8 - - + -
4190F PHE* 3.5 45.0 - + + -
4985F ASN 4.0 1.2 + - - -
4986F TYR* 3.1 23.0 + + + +
4988F PHE* 1.3 79.5 - - - +
4990F LEU* 1.3 74.6 + - + +
4992F TYR* 3.2 14.1 + + + +
4993F LEU* 3.2 35.8 - - + +
5004F GLN 5.4 1.1 - - - -
5005F GLU* 5.2 5.6 - - + -
5008F VAL* 3.8 42.6 - - + -
5019F PHE* 5.7 4.0 - + - -
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Residues in contact with LEU4990 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4229F PHE* 6.2 1.3 - - + -
4230F VAL* 4.5 13.0 - - + +
4233F CYS* 4.5 23.8 - - + -
4234F GLU* 5.7 2.2 - - + +
4237F ILE* 6.4 0.4 - - - -
4714F TRP* 6.1 4.5 - - + -
4986F TYR* 3.4 17.5 + - + +
4987F MET* 3.4 8.5 + - - +
4989F PHE* 1.3 89.3 - - + +
4991F MET* 1.3 65.4 + - - +
4993F LEU* 3.3 7.7 + - + +
4994F ILE* 3.1 29.3 + - + +
5012F TYR* 4.2 32.1 - - + +
5019F PHE* 5.1 15.7 - - + -
5020F PHE* 6.4 1.1 - - + -
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Residues in contact with MET4991 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4193F SER* 5.2 5.4 - - - +
4195F THR* 6.0 5.6 - - + -
4196F ASN* 3.6 34.3 - - + +
4237F ILE* 3.7 38.8 - - + +
4987F MET 2.9 17.7 + - - +
4988F PHE 3.5 6.3 - - - +
4989F PHE 3.2 0.4 - - - -
4990F LEU* 1.3 77.2 - - - +
4992F TYR* 1.3 57.3 + - - +
4994F ILE* 4.5 8.5 - - - +
4995F ASN* 2.8 44.4 + - + +
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Residues in contact with TYR4992 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4190F PHE* 4.9 22.4 - + + -
4191F GLU* 4.1 26.9 - - + +
4988F PHE 2.9 13.8 + - - +
4989F PHE* 3.2 14.1 + + + +
4991F MET* 1.3 79.2 - - - +
4993F LEU* 1.3 69.6 - - + +
4995F ASN* 4.8 3.1 - - + -
4996F LYS* 3.1 43.0 + - + +
5000F GLU* 3.7 20.8 + - - +
5001F HIS* 5.4 1.5 - - + -
5002F THR* 6.1 1.6 - - + -
5005F GLU* 4.8 14.4 - - + -
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Residues in contact with LEU4993 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4989F PHE* 3.2 40.2 - - + +
4990F LEU* 3.3 10.2 + - + +
4991F MET 3.3 0.4 - - - -
4992F TYR* 1.3 90.7 - - + +
4994F ILE* 1.3 60.5 + - - +
4996F LYS* 3.0 17.0 - - - +
4997F ASP 5.3 0.5 - - - -
5001F HIS* 5.0 7.6 - - + -
5005F GLU* 3.4 35.9 - - + +
5008F VAL* 4.7 4.5 - - + -
5009F TRP* 3.7 45.5 - - + -
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Residues in contact with ILE4994 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3748F PHE* 5.6 18.9 - - + -
4237F ILE* 5.9 6.3 - - + -
4714F TRP* 4.6 33.0 - - + -
4990F LEU* 3.1 19.9 + - + +
4991F MET* 3.3 11.4 + - - +
4993F LEU* 1.3 77.6 - - + +
4995F ASN* 1.3 67.0 + - - +
4996F LYS 3.8 2.4 - - - +
4997F ASP* 5.6 0.2 - - - +
5009F TRP* 3.7 27.8 - - + -
5012F TYR* 5.5 6.1 - - + -
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Residues in contact with ASN4995 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4991F MET* 2.8 35.0 + - + +
4992F TYR* 4.5 2.5 - - - +
4994F ILE* 1.3 77.2 - - - +
4996F LYS* 1.3 64.1 + - - +
4997F ASP* 3.7 7.6 + - - +
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Residues in contact with LYS4996 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4992F TYR* 3.1 37.7 + - + +
4993F LEU* 3.0 21.9 - - - +
4994F ILE 3.8 2.8 - - - +
4995F ASN* 1.3 83.3 - - - +
4997F ASP* 1.3 67.3 + - - +
5000F GLU* 4.4 14.6 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il